Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming
Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming
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DOI：
10.1111/syen.12508
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发表时间：
2021-10
影响因子：
4.8
通讯作者：
Alexandros Vasilikopoulos;M. Balke;Sandra Kukowka;James M. Pflug;S. Martin;K. Meusemann;L. Hendrich;C. Mayer;D. Maddison;O. Niehuis;R. Beutel;B. Misof
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作者：
Alexandros Vasilikopoulos;M. Balke;Sandra Kukowka;James M. Pflug;S. Martin;K. Meusemann;L. Hendrich;C. Mayer;D. Maddison;O. Niehuis;R. Beutel;B. Misof
Adephaga是鞘翅目的第二大亚目，包含水生和陆生类群，有时分别被归类为Hydrodephaga和Geadephaga。Adephaga的系统发育关系已被深入研究，但Geadephaga的主要亚群的关系和Hygrobiidae在Dytiscoidea中的位置仍然不清楚。在这里，我们推断新的DNA杂交诱饵的外显子捕获基因组学，我们联合收割机新的杂交捕获序列数据与转录组产生最大的Adephaga内的基因组分类群采样。我们的分析表明，新的诱饵是适合捕捉不同谱系的Adephaga的目标位点。适度修剪的超矩阵的系统发育分析证实了并系'Hydrodephaga'的假设，与Gyrinidae作为所有其他家庭的姐妹，如在基于形态学的同源性，即使四重一致性分析不支持这一结果。所有的分析与网站异质模型表明Trachypachidae作为姐妹分支步甲科+ Cicindelidae在一致的结果从形态学研究。Haliplidae被推断为Dytiscoidea的姐妹，而Noteridae（+最有可能Meruidae）的一个分支被推断为所有剩余Dytiscoidea的姐妹。一个强有力的支持分支Hygrobiidae +（Amphalidae+单系Aspidytidae）推断在大多数分析适度修剪超矩阵时，使用站点异质模型。在一般情况下，我们发现，严格修剪超矩阵的结果减少偏离模型假设，但也减少系统发育信息。我们还发现，位点异质C60模型在不同氨基酸超矩阵的分析中提供了比位点同质模型更大的Adephaga系统发育关系的稳定性。因此，位点异质性C60模型可以潜在地减少基因组学中的不一致性。最后，我们发现基因树错误在数据中很突出，即使在对基因进行子采样以减少这些错误之后，但我们还表明，在汇总合并分析中基于似然映射标准的子采样基因会导致与基于级联的树的拓扑一致性更高。总的来说，我们的分析表明，适度的比对修剪策略，位点异质模型的应用和基因树错误的缓解应常规地包括在基因组序列中，以便更准确地推断物种的遗传。
Adephaga is the second largest suborder of Coleoptera and contains aquatic and terrestrial groups that are sometimes classified as Hydradephaga and Geadephaga, respectively. The phylogenetic relationships of Adephaga have been studied intensively, but the relationships of the major subgroups of Geadephaga and the placement of Hygrobiidae within Dytiscoidea remain obscure. Here, we infer new DNA‐hybridization baits for exon‐capture phylogenomics and we combine new hybrid‐capture sequence data with transcriptomes to generate the largest phylogenomic taxon sampling within Adephaga presented to date. Our analyses show that the new baits are suitable to capture the target loci across different lineages of Adephaga. Phylogenetic analyses of moderately trimmed supermatrices confirm the hypothesis of paraphyletic ‘Hydradephaga’, with Gyrinidae placed as sister to all other families as in morphology‐based phylogenies, even though quartet‐concordance analyses did not support this result. All analyses conducted with site‐heterogeneous models suggest Trachypachidae as sister to a clade Carabidae + Cicindelidae in congruence with results from morphological studies. Haliplidae is inferred as sister to Dytiscoidea, while a clade of Noteridae (+ most likely Meruidae) is inferred as sister to all remaining Dytiscoidea. A strongly supported clade Hygrobiidae + (Amphizoidae + monophyletic Aspidytidae) is inferred in most analyses of moderately trimmed supermatrices when a site‐heterogeneous model is used. In general, we find that stringent trimming of supermatrices results in reduced deviation from model assumptions but also in reduction of phylogenetic information. We also find that site‐heterogeneous C60 models provide greater stability of phylogenetic relationships of Adephaga across analyses of different amino‐acid supermatrices than site‐homogeneous models. Thus, site‐heterogeneous C60 models can potentially reduce incongruence in phylogenomics. Lastly, we show that gene‐tree errors are prominent in the data, even after sub‐sampling genes to reduce these errors, but we also show that subsampling genes based on the likelihood mapping criterion in summary coalescent analyses results in higher topological congruence with the concatenation‐based tree. Overall, our analyses demonstrate that moderate alignment trimming strategies, application of site‐heterogeneous models and mitigation of gene‐tree errors should be routinely included in the phylogenomic pipeline in order to more accurately infer the phylogeny of species.